arcs at the tail side are drawn from the middle, while position of arrow at the head side is computed to exactly touch vertex border

That works fine when vertices are drawn opaque.
But when vertices are drawn transparently such rules produce the following picture:

To prevent lines to be visible inside vertices, we must compute exact intercept of
lines and vertices border. In Pajek we demand that by checking
Export / Options / EPS, SVG: Lines finished at Vertex Border.
In this way we obtain the following picture:

Note:If edges/arcs are too thick the only way to get nice picture is to draw lines from the middle of the vertices -
vertices should be drawn opaque.